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Is it currently possible to parameterize small (drug) molecules that have net charge != 0 with sage2? #13

Closed josephdepaoloboisvert closed 1 year ago

josephdepaoloboisvert commented 2 years ago

I attempted to parameterize a library of drug molecules by following the toolkit-showcase examples, however, only those that were neutrally charged were successfully parameterized with the openff-2.0.0 parameters. The positively charged molecules all raised an error regrading the extra protonation of a nitrogen (the protonation of these sites is intended however).

j-wags commented 2 years ago

There should be no problem parametrizing molecules with net charge. Could you post the SMILES or SDF of the molecule that you're having trouble with? And could you post the error that comes out?